The way I set it up, is each scrubber has only one recipe and can only accept the correct filter. When the scrubber is placed on the map, the appropriate filter for that scrubber is automatically selected. In the game, without editing the source files, there is no way to put a charcoal filter into a water scrubber.
Although the two filters can selected and processed in chemical plants, they just generate pollution based on the chemical plant. Using the vanilla chemical plant, 4 pollution per second will be generated, vs 45 or 135 removed from correct scrubber.
I'll take a look into that next time I touch this mod.
